|
| Status |
Public on Aug 31, 2020 |
| Title |
phs001866_AP_145 |
| Sample type |
SRA |
| |
|
| Source name |
breast
|
| Organism |
Homo sapiens |
| Characteristics |
tumor_type: primary tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor tissue was disrupted using roto-stator homogenization. RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to manufacturer protocol. RNA was quantified using a NanoDrop® Spectrophotometer, and the quality of RNA was then analyzed via 2100 Bioanalyzer Instrumentwhich using the RNA 6000 Nano assay (Agilent) for determination of an RNA Integrity Number (RIN).
Briefly, 1 μg of total RNA was converted to RNAseq libraries using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced on an Illumina HiSeq 2500 using a 2x50bp configuration with an average of 136 million read pairs per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA-Seq of human breast primary tumor
|
| Data processing |
Quality-control-passed reads were aligned to the human reference CGRh38/hg38 genome using STAR.
The alignment profile was determined by Picard Tools v1.64 (http://broadinstitute.github.io/picard/). Transcript abundance estimates for each sample were performed using Salmon, an expectation-maximization algorithm using the UCSC gene definitions.
Genome_build: CGRh38/hg38 genome
Supplementary_files_format_and_content: Raw read counts for all RNAseq samples were normalized to a fixed upper quartile (166_AP206_UQN.final.tsv). RNAseq normalized gene counts from primary and metastatic tumors were log2 transformed, the zeros were added again after log transformation and the genes were filtered for those expressed in 70% of samples using the cluster 3.0 software and the samples were median centered. (166_AP206_UQN_w0_log2_70p_mdctr.final.tsv)
|
| |
|
| Submission date |
Mar 20, 2020 |
| Last update date |
Aug 31, 2020 |
| Contact name |
Charles M. Perou |
| E-mail(s) |
cperou@med.unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
|
| Street address |
12-044 Lineberger Comprehensive Cancer Center CB# 7295
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE147322 |
FGFR4 is a regulator of tumor subtype differentiation in luminal breast cancer and metastatic disease II |
|
| Relations |
| BioSample |
SAMN13494125 |
| SRA |
SRX7513872 |
